First of all, thank you for the quick response! I should have been more specific in my question: My issue is when I send the new version of the books (going through the manage my kindle purchases on the website, and send it to kindle on my PC), it doesn't actually send me a new .AZW file, so I have nothing to drag and drop into calibre. And it's not updating the file on my computer as I sort by date modified, and nothing seems to be changing.

UPDATE: every once in a while it updates...I've just been doing a trial and error thing where I send the book like 10 times to my kindle for PC and wait for it to show up as an updated file in my documents!

Ah, it's the getting the updated book that's the issue. Sorry, I can't help you there.